build_gbm_se: use curatedTCGAData and Brennan metadata to build an...

In vjcitn/BiocAIML: AI and ML excursions with Bioconductor and tidymodels

Description

use curatedTCGAData and Brennan metadata to build an annotated GBM MAE

Usage

build_gbm_se(cache = BiocFileCache::BiocFileCache())

Arguments

cache

if not NULL, location of BiocFileCache instance

Note

Will cache the created SummarizedExperiment instance unless told not to. 'rname' is '"brenn_gbm_se"'.

Examples

gbmse = build_gbm_se()

# check effect of MGMT methylation on survival

xm = gbmse[, gbmse$mgmt_status !="" & gbmse$vital_status !=""]
library(survival)
ss = Surv(xm$os_days, 1*(xm$vital_status=="DECEASED"))
plot(survfit(ss~xm$mgmt_status), lty=1:2)
legend(1100, .95, lty=c(1,2), legend=c("MGMT methylated", "unmethylated"))
title("Time-on-study/vital status for 123 GBM patients analyzed in Brennan et al. PMID 24120142")
survdiff(ss~xm$mgmt_status)

vjcitn/BiocAIML documentation built on Dec. 23, 2021, 4:05 p.m.